Distributed Holistic Clustering on Linked Data

Link discovery is an active field of research to support data integration in the Web of Data. Due to the huge size and number of available data sources, efficient and effective link discovery is a very challenging task. Common pairwise link discovery approaches do not scale to many sources with very large entity sets. We here propose a distributed holistic approach to link many data sources based on a clustering of entities that represent the same real-world object. Our clustering approach provides a compact and fused representation of entities, and can identify errors in existing links as well as many new links. We support a distributed execution of the clustering approach to achieve faster execution times and scalability for large real-world data sets. We provide a novel gold standard for multi-source clustering, and evaluate our methods with respect to effectiveness and efficiency for large data sets from the geographic and music domains

Large Scale Clustering with Variational EM for Gaussian Mixture Models

How can we efficiently find large numbers of clusters in large data sets with high-dimensional data points? Our aim is to explore the current efficiency and large-scale limits in fitting a parametric model for clustering to data distributions. To do so, we combine recent lines of research which have previously focused on separate specific methods for complexity reduction. We first show theoretically how the clustering objective of variational EM (which reduces complexity for many clusters) can be combined with coreset objectives (which reduce complexity for many data points). Secondly, we realize a concrete highly efficient iterative procedure which combines and translates the theoretical complexity gains of truncated variational EM and coresets into a practical algorithm. For very large scales, the high efficiency of parameter updates then requires (A) highly efficient coreset construction and (B) highly efficient initialization procedures (seeding) in order to avoid computational bottlenecks. Fortunately very efficient coreset construction has become available in the form of light-weight coresets, and very efficient initialization has become available in the form of AFK-MC$^2$ seeding. The resulting algorithm features balanced computational costs across all constituting components. In applications to standard large-scale benchmarks for clustering, we investigate the algorithm's efficiency/quality trade-off. Compared to the best recent approaches, we observe speedups of up to one order of magnitude, and up to two orders of magnitude compared to the $k$-means++ baseline. To demonstrate that the observed efficiency enables previously considered unfeasible applications, we cluster the entire and unscaled 80 Mio. Tiny Images dataset into up to 32,000 clusters. To the knowledge of the authors, this represents the largest scale fit of a parametric data model for clustering reported so far

An Efficient Algorithm for Clustering of Large-Scale Mass Spectrometry Data

High-throughput spectrometers are capable of producing data sets containing thousands of spectra for a single biological sample. These data sets contain a substantial amount of redundancy from peptides that may get selected multiple times in a LC-MS/MS experiment. In this paper, we present an efficient algorithm, CAMS (Clustering Algorithm for Mass Spectra) for clustering mass spectrometry data which increases both the sensitivity and confidence of spectral assignment. CAMS utilizes a novel metric, called F-set, that allows accurate identification of the spectra that are similar. A graph theoretic framework is defined that allows the use of F-set metric efficiently for accurate cluster identifications. The accuracy of the algorithm is tested on real HCD and CID data sets with varying amounts of peptides. Our experiments show that the proposed algorithm is able to cluster spectra with very high accuracy in a reasonable amount of time for large spectral data sets. Thus, the algorithm is able to decrease the computational time by compressing the data sets while increasing the throughput of the data by interpreting low S/N spectra.Comment: 4 pages, 4 figures, Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference o

CLIC: clustering analysis of large microarray datasets with individual dimension-based clustering

Large microarray data sets have recently become common. However, most available clustering methods do not easily handle large microarray data sets due to their very large computational complexity and memory requirements. Furthermore, typical clustering methods construct oversimplified clusters that ignore subtle but meaningful changes in the expression patterns present in large microarray data sets. It is necessary to develop an efficient clustering method that identifies both absolute expression differences and expression profile patterns in different expression levels for large microarray data sets. This study presents CLIC, which meets the requirements of clustering analysis particularly but not limited to large microarray data sets. CLIC is based on a novel concept in which genes are clustered in individual dimensions first and in which the ordinal labels of clusters in each dimension are then used for further full dimension-wide clustering. CLIC enables iterative sub-clustering into more homogeneous groups and the identification of common expression patterns among the genes separated in different groups due to the large difference in the expression levels. In addition, the computation of clustering is parallelized, the number of clusters is automatically detected, and the functional enrichment for each cluster and pattern is provided. CLIC is freely available at http://gexp2.kaist.ac.kr/clic

Data mining and database systems: integrating conceptual clustering with a relational database management system.

Many clustering algorithms have been developed and improved over the years to cater for large scale data clustering. However, much of this work has been in developing numeric based algorithms that use efficient summarisations to scale to large data sets. There is a growing need for scalable categorical clustering algorithms as, although numeric based algorithms can be adapted to categorical data, they do not always produce good results. This thesis presents a categorical conceptual clustering algorithm that can scale to large data sets using appropriate data summarisations. Data mining is distinguished from machine learning by the use of larger data sets that are often stored in database management systems (DBMSs). Many clustering algorithms require data to be extracted from the DBMS and reformatted for input to the algorithm. This thesis presents an approach that integrates conceptual clustering with a DBMS. The presented approach makes the algorithm main memory independent and supports on-line data mining

Estimation of instrinsic dimension via clustering

The problem of estimating the intrinsic dimension of a set of points in high dimensional space is a critical issue for a wide range of disciplines, including genomics, finance, and networking. Current estimation techniques are dependent on either the ambient or intrinsic dimension in terms of computational complexity, which may cause these methods to become intractable for large data sets. In this paper, we present a clustering-based methodology that exploits the inherent self-similarity of data to efficiently estimate the intrinsic dimension of a set of points. When the data satisfies a specified general clustering condition, we prove that the estimated dimension approaches the true Hausdorff dimension. Experiments show that the clustering-based approach allows for more efficient and accurate intrinsic dimension estimation compared with all prior techniques, even when the data does not conform to obvious self-similarity structure. Finally, we present empirical results which show the clustering-based estimation allows for a natural partitioning of the data points that lie on separate manifolds of varying intrinsic dimension

Cosine-Based Clustering Algorithm Approach

Due to many applications need the management of spatial data; clustering large spatial databases is an important problem which tries to find the densely populated regions in the feature space to be used in data mining, knowledge discovery, or efficient information retrieval. A good clustering approach should be efficient and detect clusters of arbitrary shapes. It must be insensitive to the outliers (noise) and the order of input data. In this paper Cosine Cluster is proposed based on cosine transformation, which satisfies all the above requirements. Using multi-resolution property of cosine transforms, arbitrary shape clusters can be effectively identified at different degrees of accuracy. Cosine Cluster is also approved to be highly efficient in terms of time complexity. Experimental results on very large data sets are presented, which show the efficiency and effectiveness of the proposed approach compared to other recent clustering methods